As I mentioned before the Windows install of Inkscape does have the preference file. Mine is located at C:\Users\xxUsernamexx\AppData\Roaming\inkscape\preferences.xml. I posted a link to the directions for how to find this location. There should be an easy way to find it in a Perl script.
Update: You can find that location in your script with $ENV{APPDATA} which equals C:\Users\xxUsernamexx\AppData\Roaming.
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